1. Highlights
● produced in 2007
● 11 new directives and 34 new procedures
● fit regressions, curves and nonlinear models when the residuals have an AR1 structure or have correlations defined by a power-distance model (RAR1 and NLAR1)
● fit a quadratic surface and estimate its stationary point (RQUADRATIC)
● circular regression (RCIRCULAR)
● meta analysis to form fixed or random combined estimates using results saved from individual trials (META)
● Cochran-Mantel-Haenszel test (CMHTEST)
● no limit on the number of comparison contrasts fitted by ANOVA, regression contrasts limited only by the number of d.f. of the factor whose contrasts are being calculated
● F statistics for fixed terms in REML
● produce experimental designs efficient under analysis of covariance (COVDESIGN)
● hierarchical generalized nonlinear models (HGNONLINEAR)
● negative-binomial distribution and logratio link in generalized estimating equations (GEE) and generalized linear mixed models (GLMM)
● estimate parameters of beta binomial distribution (BBINOMIAL)
● estimate false discovery rate by Bonferroni-type procedure (FDRBONFERRONI)
● MCMC analyses by running the WinBUGS or OpenBUGS systems from GenStat (BGXGENSTAT)
● redundancy analysis (RDA)
● species accumulation curves (ECACCUMULATION)
● Shapiro-Wilk test for Normality (WSTATISTIC)
● least significant intervals (SEDLSI)
● enhanced text manipulation: break a text up into individual words (TXBREAK), construct a text by apppending or concatenating values from other variates, factors, texts or pointers (TXCONSTRUCT), search for a sub-text within a text (TXFIND), or search for strings in the lines of a text (TXPOSITION)
● form multiple-response factors from free-response data (FFREERESPONSEFACTOR)
● tabulation of skewness and kurtosis coefficients (TABULATE)
● generalized linear models and bootstrap analysis of survey data (SVBOOT and SVGLM)
● control over which margins to print of tables (PRINT)
● plots of one- or two-way tables of means from REML (VGRAPH)
● enhanced graphics customization: outlines of bar charts (BARCHART), histograms (DHISTOGRAM) and pie charts (DPIE); annotation of contour lines by their heights (DCONTOUR); boxes around keys and surfaces (FRAME); styles of grids in shade plots (DSHADE); shading of the sides of surfaces (DSURFACE); more control over the positions of the x-, y- and z-axes, and of the sizes of the margins between the ends of the axes and the lowest/highest plotted points (XAXIS, YAXIS and ZAXIS)
● add annotation to graphs (DTEXT)
● create, save and reload custom graphics environments (DLOAD and DSAVE)
● define 256 different colours for graphics (previously 64; see COLOUR)
● define 256 different graphics pens (previously 64; see PEN)
2. What’s new
2.1 Directives
BARCHART plots bar charts in high-resolution graphics.
CALLS lists library procedures called by a procedure.
DLOAD loads the graphics environment settings from an external file.
DSAVE saves the current graphics environment settings to an external file.
LPCONTOUR produces contour maps of two-way arrays of numbers using character (i.e. line-printer) graphics. This is a synonym of the existing CONTOUR directive, which may be modified to use high-resolution graphics in a future release.
LPGRAPH produces point and line plots using character (i.e. line-printer) graphics. This is a synonym of the existing GRAPH directive, which may be modified to use high-resolution graphics in a future release.
LPHISTOGRAM produces histograms using character (i.e. line-printer) graphics. This is a synonym of the existing HISTOGRAM directive, which may be modified to use high-resolution graphics in a future release.
TXBREAK breaks up a text structure into individual words.
TXCONSTRUCT forms a text structure by appending or concatenating values of scalars, variates, texts, factors or pointers; allows the case of letters to be changed or values to truncated and reversed.
TXFIND finds a subtext within a text structure.
TXPOSITION locates strings within the lines of a text structure.
2.2 Procedures
AMCOMPARISON performs pairwise multiple comparison tests for ANOVA means.
BBINOMIAL estimates the parameters of the beta binomial distribution.
BGIMPORT imports MCMC output in CODA format produced by WinBUGS or OpenBUGS.
BGPLOT produces plots for output and diagnostics from MCMC simulations.
BGXGENSTAT runs WinBUGS from GenStat in batch mode using scripts.
CMHTEST performs the Cochran-Mantel-Haenszel test.
COVDESIGN produces experimental designs efficient under analysis of covariance.
DCOVARIOGRAM plots 2-dimensional auto- and cross-variograms.
DOTHISTOGRAM plots dot histograms.
DTEXT adds text to a graph.
DVARIOGRAM plots fitted models to an experimental variogram.
ECACCUMULATION plots species accumulation curves for samples or individuals.
FACLEVSTANDARDIZE redefines a list of factors so that they have the same levels or labels.
FCORRELATION forms the correlation matrix for a list of variates.
FDRBONFERRONI estimates false discovery rates by a Bonferroni-type procedure.
FFREERESPONSEFACTOR forms multiple-response factors from free-response data.
GETNAME forms the name of a structure according to its IPRINT attribute.
HGNONLINEAR defines nonlinear parameters for the fixed model of a hierarchical generalized linear model.
LSIPLOT plots least significant intervals, saved from SEDLSI.
META combines estimates from individual trials.
MIN1DIMENSION finds the minimum of a function in one dimension.
NLAR1 fits curves with an AR1 or a power-distance correlation model.
PDUPLICATE duplicates a pointer, with all its components.
PTROTATE rotates a point pattern.
RAR1 fits regressions with an AR1 or a power-distance correlation model.
RCIRCULAR does circular regression of mean direction for an angular response.
RDA performs redundancy analysis.
RQUADRATIC fits a quadratic surface and estimates its stationary point.
SAGRAPES produces statistics and graphs for checking sensory panel performance.
SEDLSI calculates least significant intervals.
SVBOOT bootstraps data from random surveys.
SVGLM fits generalized linear models to survey data.
VGRAPH plots one- or two-way tables of means from REML.
WSTATISTIC calculates the Shapiro-Wilk test for Normality.
3. What’s changed
Most of the changes are completely compatible with Release 9, the previous release. There are a few commands, however, where new options or parameters have been inserted into the existing lists. These may cause problems in statements where option or parameter names have been omitted or abbreviated (see Section 1.7.1 of Part 1 of the Guide to the GenStat Command Language for details). To avoid any difficulty, the name of the option/parameter after the new option/parameter should be given explicitly, and not abbreviated to fewer than four characters.
Any command, where changes in Release 10 may cause incompatibilities in existing programs, is marked in Sections 3.1 and 3.2 by the symbol †. The full details are given in Section 3.3.
3.1 Directives
ANOVA now has no limit on the number of comparisons that can be made between levels of a factor using the COMPARISON function.
†DCONTOUR can now annotate the contours by their heights (as an alternative to an integer indexing a list of contour heights in the key).
†DHISTOGRAM allows you to control the use and appearance of the lines drawing the outlines around the bars or the perimeter of the plot.
†DPIE allows you to control the use and appearance of the lines drawing the outlines around the slices or the perimeter of the pie chart. It also allows you to control how the slices are annotated in the description.
†DSURFACE allows you to shade the sides of the surface.
†DSHADE allows to to control the way in which the grid is drawn.
FCLASSIFICATION can now reorder the terms in the model; in particular, this means that a term that is marginal to an earlier term will be moved to come before it, rather than being deleted.
FITCURVE allows for weight matrices, provided these do not define non-zero covariances between groups, if any are defined (by a factor in the model).
†FRAME can control the sizes of boxes to draw around keys, and the position of the graph title.
PREDICT allows classifying factors to be specified to run in parallel with other classifying factors (as in VPREDICT).
PRINT allows you to print only some of the margins of tables, can now omit lines of tables that contain only missing values.
†REML and VDISPLAY have a new option FMETHOD to control the production of F-statistics for fixed terms.
†RKEEP has an option IGNOREFAILURE that allows you to save information from generalized linear models that have not have fitted successfully.
TABULATE can form tables of skewness and kurtosis coefficients, and of standard errors of means.
TERMS can print monitoring information from the fitting of the null model that contains just a constant.
†XAXIS, †YAXIS and †ZAXIS provide more control over the positions of the x-, y- and z-axes, and of the sizes of the margins between the ends of the axes and the lowest/highest plotted points.
3.2 Procedures
A2DISPLAY, †A2WAY and †A2KEEP have a new option RMETHOD to control the type of residuals (simple or standardized) that are formed.
can plot residuals from any stratum (error term), not just from the final residual term, and the user can supply an overall title (to use instead of the identifier of the y-variate).
AFIELDRESIDUALS can now produce shade plots and can now plot standardized residuals from the final stratum (as an alternative to simple residuals).
†AGRAPH can now plot bar charts, and also now allows e.s.e.’s or l.s.d.’s to be used instead of s.e.d.’s.
AMTDISPLAY and †AMTIER now allow the choice of whether to combine sets of pseudo-terms in the analysis-of-variance table or present them in separate lines.
†AMTIER now allows you to constrain the type of balance within the second and third structure formulae.
†AREPMEASURES allows numbers or labels to be specified to identify the time points in the output.
†A2KEEP has a new option RMETHOD to control the type of residuals (simple or standardized) that are saved.
CENSOR has a new option MAXCYCLE to control the number of iterations.
CVAPLOT has new options CREGION and CIPROBABILITY to control the type and size of confidence region.
†GEE now allows the negative-binomial distribution and logratio link.
†GLMM now allows the negative-binomial distribution and logratio link.
†HGFIXEDMODEL has a new option DLINK to allow a reciprocal link function to be selected instead of the log link for the dispersion model for phi, and a new option DOFFSET to include an offset there.
†HGPLOT has a new option DHGRANDOMTERM to plots to be produced for random model terms in the HGLM modelling the dispersion in a DHGLM.
†HGRANDOMMODEL has a new parameter DLINK to allow a reciprocal link function to be selected instead of the log link for the dispersion models for the random terms, and a new option DOFFSET to include offsets there.
MAANOVA now allows the limits for contrasts and deviations to be changed from the default (ANOVA) values.
MTABULATE can form tables of standard deviations, skewness and kurtosis coefficients, and of standard errors of means.
PARTIALCORRELATIONS can now calculate weighted correlations.
TTEST can now calculate weighted t-tests.
3.3 Incompatibilities
A2WAY procedure |
option RMETHOD inserted before EXIT. |
|---|---|
A2KEEP procedure |
option RMETHOD inserted before EXIT. |
AGRAPH procedure |
options PSE and LSDLEVEL inserted before SAVE. |
AMTIER procedure |
options F2BALANCE and F3BALANCE inserted before PSEUDOTERMS. |
AREPMEASURES procedure |
TIMEPOINTS option inserted before FPROBABILITY option. |
AUKEEP procedure |
option RMETHOD inserted before SAVE. |
CONTOUR directive |
may be replaced by a high-resolution graphics version in a future release. You may wish to switch now to the LPCONTOUR directive (which has the same syntax) to avoid future incompatibilities. |
DCONTOUR |
option ANNOTATION inserted before SCREEN. |
DHISTOGRAM |
options OUTLINE and PENOUTLINE inserted before SCREEN. |
DPIE |
options ANNOTATION, OUTLINE and PENOUTLINE inserted before SCREEN. |
DSURFACE |
option PENSIDE inserted before NCONTOURS. |
DSHADE |
option PENGRID inserted before SCREEN. |
FRAME directive |
options BOXSURFACE and BOXKEY inserted before PENTITLE, and option TPOSITION inserted before SAVE. |
GEE procedure |
options AGGREGATION and KLOGRATIO inserted before QUADESTIMATION. |
GLMM procedure |
options AGGREGATION and KLOGRATIO inserted before OWNDIST. |
GRAPH directive |
may be replaced by a high-resolution graphics version in a future release. You may wish to switch now to the LPGRAPH directive (which has the same syntax) to avoid future incompatibilities. |
HGFIXEDMODEL procedure |
option DLINK inserted before DTERMS. |
HGPLOT procedure |
parameter DHGRANDOMTERM inserted before RMETHOD. |
HGRANDOMMODEL procedure |
parameter DLINK inserted before DFORMULA, and parameter DOFFSET inserted before LMATRIX. |
HISTOGRAM directive |
may be replaced by a high-resolution graphics version in a future release. You may wish to switch now to the LPHISTOGRAM directive (which has the same syntax) to avoid future incompatibilities. |
REML directive |
option FMETHOD inserted before WORKSPACE. |
RKEEP directive |
option IGNOREFAILURE inserted before SAVE. |
XAXIS directive |
options MLOWER%, MUPPER%, DECIMALS, YOMETHOD and ZOMETHOD inserted before SAVE. |
YAXIS directive |
options MLOWER%, MUPPER%, DECIMALS, XOMETHOD and ZOMETHOD inserted before SAVE. |
ZAXIS directive |
options MLOWER%, MUPPER%, DECIMALS, XOMETHOD and YOMETHOD inserted before SAVE. |